genomes 开源项目推荐（68 个）

tariqdaouda /pyGeno

个性化基因组学与蛋白质组学。主食：Ensembl，配菜：SNP

AIRI-Institute /GENA_LM

GENA-LM is a transformer masked language model trained on human DNA sequence.

refresh-bio /agc

Assembled Genomes Compressor (AGC) squeezing 290 GB of Human Pangenome Project assemblies down to <1.5 GB (>190× ratio), with sample and contig extraction in seconds.

pirovc /genome_updater

genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.

broadinstitute /gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

kjolley /BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

kishwarshafin /helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

BioJulia /GenomeGraphs.jl

面向 Julia 的现代基因组学框架

glarue /jgi-query

A simple command-line tool to download data from Joint Genome Institute databases

karel-brinda /MiniPhy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

karel-brinda /Phylign

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

guyleonard /get_jgi_genomes

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

stuckinaboot /iGenomics

The first app for Mobile DNA Sequence Alignment and Analysis

orangeSi /GSSplayground

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…

cumbof /MetaSBT

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

ioerger /transit

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

robinvanderlee /positive-selection

Scripts and procedures for detecting positively selected genes and codons in primates

SouthGreenPlatform /GeMo

A mosaic genome painting tool for plant genomes

NickJD /StORF-Reporter

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

debbiemarkslab /BEAR

This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"